This research proposal describes a 5-year mentored research project that has the goal of understanding how commensal bacteria impact the intestinal innate immune system. This project will build upon the principal investigator's background in microbiology, mucosal immunology, and infectious diseases. Successful completion of the research project will enable the principal investigator to gain the skills needed to secure independent funding and transition into an independent physician-scientist who continues to focus on the nexus between host-commensal interactions and the immune system. A combination of didactic and practical training detailed in the comprehensive career development plan will provide the principal investigator with an enhanced background in host-bacterial relationships, training in the analysis and interpretation of large datasets (e.g., next-generation sequencing and gene expression-profiling data), and increased experience working with gnotobiotic mice. The proposed research will take place at Harvard Medical School in the laboratory of Dr. Dennis Kasper-a world leader in studying the interface between commensal bacteria and host immunity; the research work will benefit from the availability within the Harvard community of abundant scientific resources and numerous colleagues with expertise in all fields related to the proposed work. The proposed research aims to identify novel immunomodulatory commensal bacteria. Although it has been known for more than half a century that commensal organisms-which are 10 times more abundant than host cells in the human body-are critical for proper development of the host immune system, only 4 commensal bacteria with immunomodulatory properties have been identified thus far; all of these examples affect the adaptive immune system specifically. This proposal aims to use a novel strategy of co-housing gnotobiotic mice that differ in their bacteria and the maturation state of their intestinal immune system to bioinformatically identify bacteria that are able to modulate innate immune responses. Clonally arrayed, taxonomically defined culture collections will be derived from relevant mouse strains and will allow the immunomodulatory effects of these commensal organisms to be validated. Finally, gene expression-profiling and immunophenotyping experiments will characterize the immunological changes induced by these bacteria. Ultimately, these experiments will shed light on the interplay between the microbiota and the innate immune system and offer insight into the veracity of the hygiene hypothesis. Moreover, identification of specific immunomodulatory bacteria offers the potential of novel therapies for a variety of inflammatory conditions, such as inflammatory bowel disease, arthritis, and multiple sclerosis.